From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add Ribotaper. Date: Thu, 7 Jul 2016 11:26:29 +0200 Message-ID: <20160707092629.23884-2-ricardo.wurmus@mdc-berlin.de> References: <20160707092629.23884-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37038) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bL5a7-00020V-61 for guix-devel@gnu.org; Thu, 07 Jul 2016 05:26:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bL5a3-00030u-Uq for guix-devel@gnu.org; Thu, 07 Jul 2016 05:26:51 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:60311) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bL5a3-00030h-Ns for guix-devel@gnu.org; Thu, 07 Jul 2016 05:26:47 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 43A5412A6ED for ; Thu, 7 Jul 2016 11:26:47 +0200 (CEST) Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 3A86u1w7RNNG for ; Thu, 7 Jul 2016 11:26:42 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Thu, 7 Jul 2016 11:26:42 +0200 (CEST) In-Reply-To: <20160707092629.23884-1-ricardo.wurmus@mdc-berlin.de> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (bedtools-for-ribotaper, ribotaper): New variables. --- gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 294f4ee..c4af842 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -258,6 +258,50 @@ intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.") (license license:gpl2))) +;; Later releases of bedtools produce files with more columns than +;; what Ribotaper expects. +(define bedtools-for-ribotaper + (package (inherit bedtools) + (name "bedtools") + (version "2.18.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/arq5x/bedtools2/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf")))))) + +(define-public ribotaper + (package + (name "ribotaper") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (string-append "https://ohlerlab.mdc-berlin.de/" + "files/RiboTaper/RiboTaper_Version_" + version ".tar.gz")) + (sha256 + (base32 + "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv")))) + (build-system gnu-build-system) + (inputs + `(("bedtools" ,bedtools-for-ribotaper) + ("samtools" ,samtools-0.1) + ("r" ,r) + ("r-foreach" ,r-foreach) + ("r-xnomial" ,r-xnomial) + ("r-domc" ,r-domc) + ("r-multitaper" ,r-multitaper) + ("r-seqinr" ,r-seqinr))) + (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") + (synopsis "Define translated ORFs using ribosome profiling data") + (description + "RiboTaper is a method for defining translated ORFs using ribosome +profiling data.") + (license license:gpl3+))) + (define-public bioawk (package (name "bioawk") -- 2.8.4